diff --git a/modules/flowable-app-engine/src/main/java/org/flowable/app/engine/impl/cmd/DeployCmd.java b/modules/flowable-app-engine/src/main/java/org/flowable/app/engine/impl/cmd/DeployCmd.java
index 45a0d146caf..ce28764af46 100644
--- a/modules/flowable-app-engine/src/main/java/org/flowable/app/engine/impl/cmd/DeployCmd.java
+++ b/modules/flowable-app-engine/src/main/java/org/flowable/app/engine/impl/cmd/DeployCmd.java
@@ -91,6 +91,16 @@ protected boolean deploymentsDiffer(AppDeploymentEntity deployment, AppDeploymen
         Map<String, EngineResource> resources = deployment.getResources();
         Map<String, EngineResource> savedResources = saved.getResources();
 
+        // Check if any non-generated resource was removed in the new deployment
+        for (String savedResourceName : savedResources.keySet()) {
+            EngineResource savedResource = savedResources.get(savedResourceName);
+            if (savedResource != null && !savedResource.isGenerated()) {
+                if (!resources.containsKey(savedResourceName)) {
+                    return true;
+                }
+            }
+        }
+
         for (String resourceName : resources.keySet()) {
             EngineResource savedResource = savedResources.get(resourceName);
 
diff --git a/modules/flowable-cmmn-engine/src/main/java/org/flowable/cmmn/engine/impl/cmd/DeployCmd.java b/modules/flowable-cmmn-engine/src/main/java/org/flowable/cmmn/engine/impl/cmd/DeployCmd.java
index d9cd8d7d691..e9046d94acd 100644
--- a/modules/flowable-cmmn-engine/src/main/java/org/flowable/cmmn/engine/impl/cmd/DeployCmd.java
+++ b/modules/flowable-cmmn-engine/src/main/java/org/flowable/cmmn/engine/impl/cmd/DeployCmd.java
@@ -100,6 +100,15 @@ protected boolean deploymentsDiffer(CmmnDeploymentEntity deployment, CmmnDeploym
         Map<String, EngineResource> resources = deployment.getResources();
         Map<String, EngineResource> savedResources = saved.getResources();
 
+        // Check if any non-generated resource was removed in the new deployment (Modern Java Functional Stream)
+        boolean hasRemovedResource = savedResources.entrySet().stream()
+                .filter(entry -> entry.getValue() != null && !entry.getValue().isGenerated())
+                .anyMatch(entry -> !resources.containsKey(entry.getKey()));
+
+        if (hasRemovedResource) {
+            return true;
+        }
+
         for (String resourceName : resources.keySet()) {
             EngineResource savedResource = savedResources.get(resourceName);
 
diff --git a/modules/flowable-dmn-engine/src/main/java/org/flowable/dmn/engine/impl/cmd/DeployCmd.java b/modules/flowable-dmn-engine/src/main/java/org/flowable/dmn/engine/impl/cmd/DeployCmd.java
index d6ce57bb693..1168b12b33c 100644
--- a/modules/flowable-dmn-engine/src/main/java/org/flowable/dmn/engine/impl/cmd/DeployCmd.java
+++ b/modules/flowable-dmn-engine/src/main/java/org/flowable/dmn/engine/impl/cmd/DeployCmd.java
@@ -123,6 +123,15 @@ protected boolean deploymentsDiffer(DmnDeploymentEntity deployment, DmnDeploymen
         Map<String, EngineResource> resources = deployment.getResources();
         Map<String, EngineResource> savedResources = saved.getResources();
 
+        // Check if any non-generated resource was removed in the new deployment (Modern Java Functional Stream)
+        boolean hasRemovedResource = savedResources.entrySet().stream()
+                .filter(entry -> entry.getValue() != null && !entry.getValue().isGenerated())
+                .anyMatch(entry -> !resources.containsKey(entry.getKey()));
+
+        if (hasRemovedResource) {
+            return true;
+        }
+
         for (String resourceName : resources.keySet()) {
             EngineResource savedResource = savedResources.get(resourceName);
 
diff --git a/modules/flowable-engine/src/main/java/org/flowable/engine/impl/cmd/DeployCmd.java b/modules/flowable-engine/src/main/java/org/flowable/engine/impl/cmd/DeployCmd.java
index 865c938f787..e0a74bb406a 100644
--- a/modules/flowable-engine/src/main/java/org/flowable/engine/impl/cmd/DeployCmd.java
+++ b/modules/flowable-engine/src/main/java/org/flowable/engine/impl/cmd/DeployCmd.java
@@ -164,6 +164,16 @@ protected boolean deploymentsDiffer(DeploymentEntity deployment, DeploymentEntit
         Map<String, EngineResource> resources = deployment.getResources();
         Map<String, EngineResource> savedResources = saved.getResources();
 
+        // Check if any non-generated resource was removed in the new deployment
+        for (String savedResourceName : savedResources.keySet()) {
+            EngineResource savedResource = savedResources.get(savedResourceName);
+            if (savedResource != null && !savedResource.isGenerated()) {
+                if (!resources.containsKey(savedResourceName)) {
+                    return true;
+                }
+            }
+        }
+
         for (String resourceName : resources.keySet()) {
             EngineResource savedResource = savedResources.get(resourceName);